Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_029134020.1 A3GO_RS0114560 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000428045.1:WP_029134020.1 Length = 485 Score = 226 bits (576), Expect = 1e-63 Identities = 140/460 (30%), Positives = 233/460 (50%), Gaps = 4/460 (0%) Query: 1 MAEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTW 60 ++ + K + YINGEW+ + V NPA + +VP + A + A AF+ W Sbjct: 3 ISNLLKNQAYINGEWISADNGHTFAVTNPADNSEITRVPSLGAAETRRAIEQADLAFRCW 62 Query: 61 SKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPS 120 K R+ +L + +L+ ++E LA L+++E GK E+ GE+ G +E+ A Sbjct: 63 RKRTAQERSNLLRRWFELIMANQEALAQLLSLEQGKPLAESRGEIAYGASFIEWFAEEAK 122 Query: 121 LMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSER 180 + GD + + A D + PIGVV I P+NFP + A+A G T ++KP+ Sbjct: 123 RVYGDVIPAHAADRRFVVIKQPIGVVAAITPWNFPNAMITRKCAPAMAAGCTVVIKPAPD 182 Query: 181 TPLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNG--ILEHPEIKAISFVGSKPVGEYVYK 238 TPL L L ++AG+P GVFNV+ + V G + +P ++ +SF GS VG+ + Sbjct: 183 TPLSALALAALADEAGIPPGVFNVLPTENAVAVGGELTSNPIVRKLSFTGSTAVGKLLMS 242 Query: 239 KGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIAD 298 + + +K+V G +V +DA+++ V + + + ++G+ C+ ++E I D Sbjct: 243 QCAGTVKKVSLELGGNAPFLVFDDADIDAAVAGALASKYRNSGQTCVCTNRFLIQESIYD 302 Query: 299 EFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVS 358 EF KL V +++G L GP+I + ++ +++ + +GARL+ G+ + Sbjct: 303 EFAEKLTRAVDALQVGPALTSDSQQGPLINQAAVEKVQRHVDDAVAKGARLMTGGQRHTL 362 Query: 359 DDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSN 418 G F PTI VT EM I +E F PV + K +EAI++AN + F A + + Sbjct: 363 -GGTFYQPTILAGVTREMHIACEETFGPVAPLFSFKTEQEAIDLANDTPFGLAAYFYARD 421 Query: 419 SNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFG 458 + E ++ GM+GIN G+ A PF G K S G Sbjct: 422 IGRVWRVAEALETGMIGINEGI-ISTAVAPFGGIKESGIG 460 Lambda K H 0.318 0.136 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 517 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 487 Length of database: 485 Length adjustment: 34 Effective length of query: 453 Effective length of database: 451 Effective search space: 204303 Effective search space used: 204303 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory